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Cruz-Bautista R, Ruíz-Villafán B, Romero-Rodríguez A, Rodríguez-Sanoja R, Sánchez S. Trends in the two-component system's role in the synthesis of antibiotics by Streptomyces. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12623-z. [PMID: 37341754 DOI: 10.1007/s00253-023-12623-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023]
Abstract
Despite the advances in understanding the regulatory networks for secondary metabolite production in Streptomyces, the participation of the two-component systems (TCS) in this process still requires better characterization. These sensing systems and their responses to environmental stimuli have been described by evaluating mutant strains with techniques that allow in-depth regulatory responses. However, defining the stimulus that triggers their activation is still a task. The transmembrane nature of the sensor kinases and the high content of GC in the streptomycetes represent significant challenges in their study. In some examples, adding elements to the assay medium has determined the respective ligand. However, a complete TCS description and characterization requires specific amounts of the involved proteins that are most difficult to obtain. The availability of enough sensor histidine kinase concentrations could facilitate the identification of the ligand-protein interaction, and besides would allow the establishment of its phosphorylation mechanisms and determine their tridimensional structure. Similarly, the advances in the development of bioinformatics tools and novel experimental techniques also promise to accelerate the TCSs description and provide knowledge on their participation in the regulation processes of secondary metabolite formation. This review aims to summarize the recent advances in the study of TCSs involved in antibiotic biosynthesis and to discuss alternatives to continue their characterization. KEY POINTS: • TCSs are the environmental signal transducers more abundant in nature. • The Streptomyces have some of the highest number of TCSs found in bacteria. • The study of signal transduction between SHKs and RRs domains is a big challenge.
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Affiliation(s)
- Rodrigo Cruz-Bautista
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico.
| | - Beatriz Ruíz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Alba Romero-Rodríguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico.
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Jin S, Hui M, Lu Y, Zhao Y. An overview on the two-component systems of Streptomyces coelicolor. World J Microbiol Biotechnol 2023; 39:78. [PMID: 36645528 DOI: 10.1007/s11274-023-03522-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/10/2023] [Indexed: 01/17/2023]
Abstract
The two-component system (TCS) found in various organisms is a regulatory system, which is involved in the response by the organism to stimuli, thereby regulating the internal behavior of the cell. It is commonly found in prokaryotes and is an important signaling system in bacteria. TCSs are involved in the regulation of physiological and morphological differentiation of the industrially important microbes from the genus Streptomyces, which produce a vast array of bioactive secondary metabolites (SMs). Genetic engineering of TCSs can substantially increase the yield of target SMs, which is valuable for industrial-scale production. Research on TCS has mainly been completed in the model strain Streptomyces coelicolor. In this review, we summarize the recent advances in the functional identification and elucidation of the regulatory mechanisms of various TCSs in S. coelicolor, with a focus on their roles in the biosynthesis of important SMs.
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Affiliation(s)
- Shangping Jin
- College of Bioengineering, Henan University of Technology, 100 Lianhua Street, 450001, Zhengzhou, China
| | - Ming Hui
- College of Bioengineering, Henan University of Technology, 100 Lianhua Street, 450001, Zhengzhou, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, 100 Guilin Road, 200234, Shanghai, China.
| | - Yawei Zhao
- College of Bioengineering, Henan University of Technology, 100 Lianhua Street, 450001, Zhengzhou, China.
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Sánchez de la Nieta R, Santamaría RI, Díaz M. Two-Component Systems of Streptomyces coelicolor: An Intricate Network to Be Unraveled. Int J Mol Sci 2022; 23:ijms232315085. [PMID: 36499414 PMCID: PMC9739842 DOI: 10.3390/ijms232315085] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Bacteria of the Streptomyces genus constitute an authentic biotech gold mine thanks to their ability to produce a myriad of compounds and enzymes of great interest at various clinical, agricultural, and industrial levels. Understanding the physiology of these organisms and revealing their regulatory mechanisms is essential for their manipulation and application. Two-component systems (TCSs) constitute the predominant signal transduction mechanism in prokaryotes, and can detect a multitude of external and internal stimuli and trigger the appropriate cellular responses for adapting to diverse environmental conditions. These global regulatory systems usually coordinate various biological processes for the maintenance of homeostasis and proper cell function. Here, we review the multiple TCSs described and characterized in Streptomyces coelicolor, one of the most studied and important model species within this bacterial group. TCSs are involved in all cellular processes; hence, unravelling the complex regulatory network they form is essential for their potential biotechnological application.
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Mechanisms of response to pH shock in microbial fermentation. Bioprocess Biosyst Eng 2019; 43:361-372. [PMID: 31650352 DOI: 10.1007/s00449-019-02232-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/13/2019] [Indexed: 10/25/2022]
Abstract
The following review highlights pH shock, a novel environmental factor, as a tool for the improvement of fermentation production. The aim of this review is to introduce some recent original studies on the enhancement of microbial fermentation production by pH shock. Another purpose of this review is to improve the understanding of the processes that underlie physiological and genetic differences, which will facilitate future research on the improvement of fermentation production and reveal the associated molecular mechanisms. This understanding will simultaneously promote the application of this strategy to other microbial fermentation systems. Furthermore, improvement of the cellular tolerance of genetically engineered bacteria can also be a new field of research in the future to enhance fermentation production.
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Romero-Rodríguez A, Maldonado-Carmona N, Ruiz-Villafán B, Koirala N, Rocha D, Sánchez S. Interplay between carbon, nitrogen and phosphate utilization in the control of secondary metabolite production in Streptomyces. Antonie van Leeuwenhoek 2018; 111:761-781. [PMID: 29605896 DOI: 10.1007/s10482-018-1073-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 03/21/2018] [Indexed: 12/21/2022]
Abstract
Streptomyces species are a wide and diverse source of many therapeutic agents (antimicrobials, antineoplastic and antioxidants, to name a few) and represent an important source of compounds with potential applications in medicine. The effect of nitrogen, phosphate and carbon on the production of secondary metabolites has long been observed, but it was not until recently that the molecular mechanisms on which these effects rely were ascertained. In addition to the specific macronutrient regulatory mechanisms, there is a complex network of interactions between these mechanisms influencing secondary metabolism. In this article, we review the recent advances in our understanding of the molecular mechanisms of regulation exerted by nitrogen, phosphate and carbon sources, as well as the effects of their interconnections, on the synthesis of secondary metabolites by members of the genus Streptomyces.
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Affiliation(s)
- Alba Romero-Rodríguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico.
| | - Nidia Maldonado-Carmona
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Beatriz Ruiz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Niranjan Koirala
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Diana Rocha
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
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Jiang J, Sun YF, Tang X, He CN, Shao YL, Tang YJ, Zhou WW. Alkaline pH shock enhanced production of validamycin A in fermentation of Streptomyces hygroscopicus. BIORESOURCE TECHNOLOGY 2018; 249:234-240. [PMID: 29045927 DOI: 10.1016/j.biortech.2017.10.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/03/2017] [Accepted: 10/05/2017] [Indexed: 06/07/2023]
Abstract
Validamycin A (Val-A) is produced by Streptomyces as a secondary metabolite with wide agricultural applications of controlling rice sheath blight, false smut and damping-off diseases. The effect of alkaline pH shock on enhancing Val-A production and its mechanism were investigated. A higher yield of Val-A was achieved by NaOH shock once or several times together with faster protein synthesis and sugar consumption and alkaline pH shock can increase Val-A production by 27.43%. Transcription of genes related to amino acid metabolism, carbon metabolism and electron respiratory chain was significantly up-regulated, accompanied by the substantial increase of respiratory activity and glutamate concentration. Val-A production was promoted by a series of complex mechanisms and made a response to pH stress signal, which led to the enhancement of glutamate metabolism and respiration activity. The obtained information will facilitate future studies for antibiotic yield improvement and the deep revealment of molecular mechanism.
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Affiliation(s)
- Jing Jiang
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Ya-Fang Sun
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xi Tang
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Chao-Nan He
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Ye-Lin Shao
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Ya-Jie Tang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, Hubei, China
| | - Wen-Wen Zhou
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang University, Hangzhou 310058, Zhejiang, China.
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Westhoff S, van Leeuwe TM, Qachach O, Zhang Z, van Wezel GP, Rozen DE. The evolution of no-cost resistance at sub-MIC concentrations of streptomycin in Streptomyces coelicolor. ISME JOURNAL 2017; 11:1168-1178. [PMID: 28094796 DOI: 10.1038/ismej.2016.194] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 11/07/2016] [Accepted: 11/16/2016] [Indexed: 11/09/2022]
Abstract
At the high concentrations used in medicine, antibiotics exert strong selection on bacterial populations for the evolution of resistance. However, these lethal concentrations may not be representative of the concentrations bacteria face in soil, a recognition that has led to questions of the role of antibiotics in soil environments as well as the dynamics of resistance evolution during sublethal challenge. Here we examine the evolution of resistance to sub-minimal inhibitory concentrations (sub-MIC) of streptomycin in the filamentous soil bacterium Streptomyces coelicolor. First, we show that spontaneous resistance to streptomycin causes an average fitness deficit of ~21% in the absence of drugs; however, these costs are eliminated at concentrations as low as 1/10 the MIC of susceptible strains. Using experimental evolution, we next show that resistance to >MIC levels of streptomycin readily evolves when bacteria are exposed to sub-MIC doses for 500 generations. Furthermore, the resistant clones that evolved at sub-MIC streptomycin concentrations carry no fitness cost. Whole-genome analyses reveal that evolved resistant clones fixed some of the same mutations as those isolated at high drug concentrations; however, all evolved clones carry additional mutations and some fixed mutations that either compensate for costly resistance or have no associated fitness costs. Our results broaden the conditions under which resistance can evolve in nature and suggest that rather than low-concentration antibiotics acting as signals, resistance evolves in response to antibiotics used as weapons.
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Affiliation(s)
- Sanne Westhoff
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Omar Qachach
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Zheren Zhang
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Gilles Philippus van Wezel
- Institute of Biology, Leiden University, Leiden, The Netherlands.,Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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Mechanism of the pH-induced conformational change in the sensor domain of the DraK Histidine kinase via the E83, E105, and E107 residues. PLoS One 2014; 9:e107168. [PMID: 25203403 PMCID: PMC4159317 DOI: 10.1371/journal.pone.0107168] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 08/06/2014] [Indexed: 01/20/2023] Open
Abstract
The DraR/DraK two-component system was found to be involved in the differential regulation of antibiotic biosynthesis in a medium-dependent manner; however, its function and signaling and sensing mechanisms remain unclear. Here, we describe the solution structure of the extracellular sensor domain of DraK and suggest a mechanism for the pH-dependent conformational change of the protein. The structure contains a mixed alpha-beta fold, adopting a fold similar to the ubiquitous sensor domain of histidine kinase. A biophysical study demonstrates that the E83, E105, and E107 residues have abnormally high pKa values and that they drive the pH-dependent conformational change for the extracellular sensor domain of DraK. We found that a triple mutant (E83L/E105L/E107A) is pH independent and mimics the low pH structure. An in vivo study showed that DraK is essential for the recovery of the pH of Streptomyces coelicolor growth medium after acid shock. Our findings suggest that the DraR/DraK two-component system plays an important role in the pH regulation of S. coelicolor growth medium. This study provides a foundation for the regulation and the production of secondary metabolites in Streptomyces.
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Yeo KJ, Park JW, Kim EH, Hwang E, Cheong HK. Mg2+-induced folding of the sensory domain of QseC histidine kinase from enterohemorrhagic Escherichia coli (EHEC) O157:H7. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Two-component systems in Streptomyces: key regulators of antibiotic complex pathways. Microb Cell Fact 2013; 12:127. [PMID: 24354561 PMCID: PMC3881020 DOI: 10.1186/1475-2859-12-127] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/16/2013] [Indexed: 01/16/2023] Open
Abstract
Streptomyces, the main antibiotic-producing bacteria, responds to changing environmental conditions through a complex sensing mechanism and two-component systems (TCSs) play a crucial role in this extraordinary "sensing" device.Moreover, TCSs are involved in the biosynthetic control of a wide range of secondary metabolites, among them commercial antibiotics. Increased knowledge about TCSs can be a powerful asset in the manipulation of bacteria through genetic engineering with a view to obtaining higher efficiencies in secondary metabolite production. In this review we summarise the available information about Streptomyces TCSs, focusing specifically on their connections to antibiotic production.
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Yeo KJ, Han YH, Eo Y, Cheong HK. Expression, purification, crystallization and preliminary X-ray analysis of the extracellular sensory domain of DraK histidine kinase from Streptomyces coelicolor. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:909-11. [PMID: 23908041 DOI: 10.1107/s1744309113018769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 07/06/2013] [Indexed: 11/10/2022]
Abstract
The bacterium Streptomyces coelicolor produces useful antibiotics from its secondary metabolites. DraK is a sensory histidine kinase involved in the differential regulation of antibiotics in S. coelicolor through the DraR/DraK two-component system. Here, the extracellular sensory domain of DraK was overexpressed in Escherichia coli, purified and crystallized using the sitting-drop vapour-diffusion method. The crystal diffracted to 2.2 Å resolution and belonged to space group C222₁, with unit-cell parameters a = 41.91, b = 174.50, c = 145.25 Å, α = β = γ = 90°.
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Affiliation(s)
- Kwon Joo Yeo
- Division of Magnetic Resonance, Korea Basic Science Institute, 16 Yeongudanji-Ro, Ochang, Chungbuk 363-883, Republic of Korea
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